Molecular Biology Basics

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Questions and Answers

What is the primary function of DNA polymerase?

To catalyze the joining of amino acids

To modify and transport proteins

To unzip the DNA double helix

To catalyze the joining of deoxyribonucleotide triphosphates (correct)

During which phase of the cell cycle does DNA replication occur?

S Phase (correct)

G2 Phase

M Phase

G1 Phase

What are the complementary base pairs in DNA?

A-C; T-G

G-C; T-A

A-T; G-C (correct)

C-T; A-G

Which cellular compartment is primarily responsible for translation?

Rough Endoplasmic Reticulum Signup and view all the answers

What role do Clamp-loading proteins play during DNA replication?

To coordinate leading and lagging strands synthesis Signup and view all the answers

Which process converts pre-mRNA into mRNA?

Splicing Signup and view all the answers

What occurs to misfolded proteins in the cytoplasm?

They are degraded Signup and view all the answers

What is the main structure of DNA?

Double helix formed by complementary strands Signup and view all the answers

What is the direction of DNA synthesis by all DNA Polymerases?

5′ to 3′ Signup and view all the answers

What is required for DNA polymerase to synthesize DNA?

A primer strand bonded to a template Signup and view all the answers

What is the role of DNA Primase in DNA replication?

To produce short RNA fragments that act as primers Signup and view all the answers

What reduces the error rate during DNA replication?

Base-pairing of correctly matched dNTPs Signup and view all the answers

What determines the expression of the lac operon?

Combined action of activators and repressors Signup and view all the answers

What are Okazaki fragments?

Short DNA segments synthesized on the lagging strand Signup and view all the answers

In the lac operon, what is the role of the i gene?

It encodes a repressor that binds to the operator Signup and view all the answers

How does telomerase maintain telomeres?

By catalyzing synthesis using its RNA template Signup and view all the answers

What happens when DNA primase removes the RNA primer?

An overhanging 3′ end is created Signup and view all the answers

What happens to cAMP levels when glucose levels decrease?

cAMP levels increase Signup and view all the answers

What is the main challenge that the lagging strand faces during DNA replication?

Synthesis in the opposite direction of the overall replication fork Signup and view all the answers

Which statement best describes the mechanism of enhancers in gene regulation?

Enhancers can act over long distances by bending DNA Signup and view all the answers

What complicates transcription in eukaryotic cells?

The presence of histone proteins and nucleosomes Signup and view all the answers

What is the primary function of promoters in eukaryotic transcription?

To serve as binding sites for general transcription factors Signup and view all the answers

In the absence of lactose, what is the state of the repressor protein in the lac operon?

It binds to the operator to inhibit transcription Signup and view all the answers

How does positive control affect the regulation of the lac operon?

By facilitating the binding of CAP by increasing cAMP levels Signup and view all the answers

What is the primary reason bacterial mRNAs are used immediately for protein synthesis?

Bacteria lack mRNA processing mechanisms. Signup and view all the answers

What is the role of the tryptophan repressor in bacterial gene regulation?

It inhibits the binding of RNA polymerase to the promoter. Signup and view all the answers

Which statement accurately describes mRNA regulation in eukaryotes compared to bacteria?

Eukaryotic mRNA must be exported to the cytoplasm for translation. Signup and view all the answers

What is the mechanism by which bacterial cells adapt to environmental changes concerning gene expression?

Via transcriptional regulation that works primarily at the initiation step. Signup and view all the answers

Which enzyme is responsible for cleaving lactose into glucose and galactose?

Beta-galactosidase Signup and view all the answers

What do operons allow bacteria to do in terms of gene expression?

Control clusters of genes with a single promoter. Signup and view all the answers

How does the half-life of bacterial mRNA compare to that of eukaryotic mRNA?

Bacterial mRNA typically has a much shorter half-life. Signup and view all the answers

Which of the following describes the primary function of the Lac Operon?

To regulate the synthesis of enzymes that metabolize lactose. Signup and view all the answers

What role does DNA looping play in gene regulation?

It facilitates interaction between a transcription factor at an enhancer and the RNA polymerase/Mediator complex at the promoter. Signup and view all the answers

Which component is primarily responsible for recognizing intron-exon boundaries during pre-mRNA splicing?

snRNPs Signup and view all the answers

What is alternative splicing?

A method that produces different mRNA variants from a single gene by including or excluding specific exons. Signup and view all the answers

Which of the following best describes the function of the spliceosome?

It catalyzes the splicing of introns from pre-mRNA. Signup and view all the answers

Which of the following tissues produces calcitonin gene-related peptide (CGRP)?

Hypothalamus Signup and view all the answers

What happens to the signal sequence during cotranslational targeting of secretory proteins to the ER?

It is cleaved by signal peptidase and released into the ER lumen. Signup and view all the answers

During the elongation phase of translation, which site on the ribosome does an aminoacyl tRNA first bind to?

A site Signup and view all the answers

Which factor is critical for bringing aminoacyl tRNA to the ribosome during elongation?

GTP-bound elongation factors Signup and view all the answers

What role does rRNA play during the peptide bond formation?

It mediates the formation of the peptide bond. Signup and view all the answers

Which factor is involved in the translocation step of elongation in prokaryotes?

EF-G Signup and view all the answers

What is the primary function of Dicer in the processing of microRNA?

It creates the functional form of miRNA. Signup and view all the answers

What potential consequence can arise from defective protein folding?

Formation of protein aggregates. Signup and view all the answers

Which of the following is a known role of miRNAs in cellular regulation?

Repressing the translation of specific mRNAs. Signup and view all the answers

Which miRNA is specifically mentioned as repressing the translation of Lin-14?

Lin-4 Signup and view all the answers

How many different mRNAs can a single miRNA potentially target?

Up to 100 Signup and view all the answers

What is one of the diseases associated with misfolded proteins in the brain?

Alzheimer’s disease Signup and view all the answers

Study Notes

DNA Structure

DNA is a nucleic acid composed of nucleotides.
Deoxyribose is a 5-carbon sugar.
A phosphate group (PO4) is attached to the 5' carbon of the sugar.
Nitrogenous bases include adenine, thymine, cytosine, and guanine.
A free hydroxyl group (-OH) is attached to the 3' carbon of the sugar.
Complementary base pairing: A-T; G-C
DNA forms a double helix from complementary strands.

Central Dogma

Information flows from DNA to RNA to protein.
Replication: DNA to DNA
Transcription: DNA to RNA
Translation: RNA to Proteins
These processes occur in different compartments of the cell.

DNA Replication

Every time a cell divides, its entire genome must be duplicated.
The process is quick and requires accuracy.
Watson and Crick postulated that DNA replication might be as simple as "unzipping" the helix and replacing the missing nucleotides.
DNA replication begins at discrete origins and then proceeds bidirectionally.

DNA Polymerase

DNA polymerase is the main enzyme in DNA replication.
It catalyzes the joining of deoxyribonucleotide 5'-triphosphates (dNTPs).
Discovered in E. coli in 1956 by Arthur Kornberg & colleagues using genetics and biochemistry.
Many different DNA polymerases exist in prokaryotes and eukaryotes. They play distinct roles in DNA replication and repair.
Several additional proteins are required for coordinated DNA synthesis.
These proteins include topoisomerase, helicase, primase, single-strand binding proteins, DNA polymerase III, DNA polymerase I, and ligase.

5' to 3' direction

DNA polymerases synthesize DNA only in the 5' to 3' direction.
They add new doxynucleotide triphosphates (dNTPs) only to a primer strand.
Primer strands are made of RNA.

DNA Primase

RNA primase synthesizes short RNA fragments that act as primers for DNA synthesis.
These short RNA primers then serve as primers for the extension of DNA.

Fidelity of DNA Replication

DNA polymerase helps to select the correct bases to insert during replication.
Binding correctly matched dNTPs causes conformational changes that lead to nucleotide incorporation.
Base pairing helps reduce the error rate to about 1 in 10⁵ per nucleotide.

Leading and Lagging Strands

The leading strand is synthesized continuously in the 5' to 3' direction.
The lagging strand is synthesized discontinuously as short, fragments called Okazaki fragments.
Okazaki fragments are joined together by DNA ligase.

Telomeres and Telomerase

Linear chromosomes have specialized terminal sequences called telomeres. These contain repetitive DNA sequences.
Telomere sequences are maintained by the enzyme telomerase.
Telomerase is a reverse transcriptase whose RNA template is complementary to the telomere repeat sequences.
Removes the RNA primer, which may result in a staggered end.
Creates a loop in the telomere.

Transcription (DNA to RNA)

Prokaryotes: Transcription and translation occur in the same compartment.
Eukaryotes: Transcription occurs in the nucleus, and translation in the cytoplasm.
Several different RNA polymerases and various proteins are involved.
mRNA transcripts are translated much more quickly.
Bacterial mRNA has a very short half-life.

Transcription Regulation (bacteria)

Regulation of gene expression allows a bacterial cell to adapt to environmental changes such as food sources.
Most transcriptional regulation in bacteria operates at the initiation step.
In addition to the promoter, nearly all genes (bacterial and eukaryotic) have regulatory DNA sequences.
In bacteria, this sequence is commonly referred to as an operator.

Regulation of the Tryptophan Operon (an example of bacterial gene regulation)

Several proteins are needed to synthesize tryptophan, so the cell expresses them only when tryptophan is needed.
Genes that code for these proteins are clustered together as an operon (one unit).
The tryptophan operon is controlled by a strong promoter, and will bind RNA polymerase and transcribe the operon until it is repressed.
The operon is switched off by a repressor protein (tryptophan repressor).
The tryptophan repressor protein is responsive to tryptophan levels.

Lactose Metabolism

Genes encoding the enzymes involved in lactose metabolism are expressed as a single unit, the Lac operon.
Required enzymes: beta-galactosidase (z), lactose permease (y), and transacetylase (a).
Beta-galactosidase cleaves lactose into glucose and galactose.
Lactose permease transports lactose into the cell.
Transacetylase inactivates toxic thiogalactosides along with lactose.

Regulation of the Lac Operon

The combination of activators and repressors control the lac operon.
These enzymes are expressed only when glucose is absent and lactose is present.
Two loci control transcription: (operator), adjacent to transcription initiation site, and i (i gene, not in operon).
In the lac operon, i encodes a protein that binds to the operator.
In the presence of lactose, the repressor is inactivated.
Positive control is mediated by cAMP and CAP.

Eukaryotic Transcriptional Regulation

Eukaryotic gene regulation is more complex than prokaryotic regulation.
Eukaryotic DNA is organized into chromatin, which complicates protein-DNA interaction.
Transcription and translation are temporally and spatially separated.

Eukaryotic Chromatin Structure

DNA is wound around histone proteins & non-histone regulatory proteins to form nucleosomes.
Nucleosomes and histones complicate the process of transcription (restrict access of transcription machinery to the DNA)
Chromatin structure is selectively modulated to allow transcription.

Promoters and Enhancers

Promoters are DNA-binding sites for general transcription factors.
Promoters mediate the binding of RNA polymerase II to the promoter.
Enhancers are DNA-binding sites for specific transcription factors.
Enhancers act over long distances by bending DNA to form a loop to position the enhancer closer to the promoter.

Gene Regulation at Great Distances

Enhancers, like promoters, function by binding transcription factors that regulate RNA polymerase.
DNA looping allows a transcription factor bound to a distant enhancer to interact with proteins associated with the RNA polymerase/Mediator complex at the promoter.

Post-transcriptional Regulation

Regulation occurs after the mRNA is transcribed but before translation.

Eukaryotic Genes

Eukaryotic genes contain introns and exons.
Introns are removed, and exons are joined to create mature mRNA.

Pre-mRNA Splicing

Pre-mRNAs (primary RNA transcripts) are processed by removing introns and joining exons.
snRNPs and proteins, along with other factors, catalyze splicing.
Introns are excised from the molecule, and exons are ligated, or joined, together to form the mature mRNA.
Alternative splicing creates multiple mRNA variations (distinct forms).

Translation (mRNA to protein)

Ribosomes have three binding sites (P, A, and E).
Aminoacyl tRNA binds to the A site by pairing with the next mRNA codon.
An elongation factor (EF-Tu in prokaryotes, eEF1a in eukaryotes) brings the aminoacyl tRNA to the ribosome.
Peptide bonds are formed, and the polypeptide is transferred to the A site.
The uncharged tRNA is released from the P site.
Translocation occurs to position the next codon in the A site.

Post-translational Regulation

Regulation occurs after the protein is translated.

Lin-4 microRNA (miRNA)

Lin-4 is a microRNA that represses the translation of Lin-14.

Other miRNAs

As many as 1000 miRNAs are encoded in mammals.
Each can target hundreds of different mRNAs.

Protein Folding and Quality Control

Newly synthesized proteins fold into various possible shapes.
Misfolded proteins can form aggregates.
Correct protein folding is assisted by molecular chaperones.
Incorrectly folded proteins are targeted by the proteasome, which digests them.

Defects in Protein Folding

Defects in protein folding are responsible for many diseases.
Alzheimer's disease is associated with misfolded proteins and the accumulation of amyloid-beta plaques and tau tangles.

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Description

Test your knowledge on essential molecular biology concepts, including DNA replication, translation, and protein folding. This quiz covers the key functions of DNA polymerase, the phases of the cell cycle, and more. Perfect for students of biology looking to reinforce their understanding of these fundamental processes.